Question

How do geneticist figure out where and when a gene is expressed?

How does a geneticist finds out what genes transcription are affected by a specific TF?

Answer 1

Not all genes are expressed in all tissues or cells. This is called differential gene expression. To check differential gene expression various methods like Reverse transcription Q-PCR, Western blotting, DNA microarray, Fluroscent insitu hybridization etc can be used.

In RT-PCR, mRNAs are isolated from the cell and a PCR is carried out with primers for the gene to be studied. Amplification of the gene happens in cell/tissue samples where the transcription of gene happens. In western blotting antibodies for the isolated protein are used to identify the expression. Micro arrays use hybridised cDNA probes to identify the matching mRNA samples. In situ hybridization also used probes labelled with fluorescence to identify mRNAs expressed.

To study the genes affected by a TF, the transcription factor is labelled with flurophore to identify the site where it binds. Using FISH, the positions where the TF binds can be identified, the DNA is then fragmented and then run it on the gel and sequencing is done to identify the genes.